Glossary

Bottleneck A temporary, dramatic reduction in population size that results in reduced genetic diversity.

Coalescence/divergence The separation of DNA sequences that share a common ancestor by the accumulation of nucleotide (base) substitutions. The time of divergence of DNA sequences or the time when sequences coalesce to a common ancestor can be estimated when the rate of nucleotide substitution is known.

Effective population size The actual number of individuals in a population that are reproducing.

Genetic diversity A measure of the genetic variability in a population.

Haplotype An individual mtDNA sequence.

Haplogroup A major class of mtDNA sequences in the human population.

Molecular clock The concept that mutations accumulate at an approximately constant rate in a given DNA sequence and in all its descendants so that times of divergence can be estimated from the ancestral form.

Population No definitive definition for humans. Usually taken to mean a group of individuals that share certain characteristics such as language, geography, ethnicity, phenotype - either one of these or all of them.

Phylogenetic tree A representation of the evolutionary history of a group of taxa, genes or other inherited markers.

The fact that ancient deoxyribonucleic acid (DNA) extracted from archaeological material can give information about past peoples, animals, and plants has been readily grasped by archaeologists. What seems to be more difficult to accept is that DNA sampled from present-day populations can also give information about that population’s history. DNA is inherited from our parents, and in turn they inherited their DNA from their parents, and so forth back into time. But with each generation the DNA packaged into the chromosomes gets ‘shuffled’ - this is known as recombination. We do not as yet have the mathematical and computing tools to ‘unravel’ the shuffling, so geneticists who are interested in population history and human evolution tend to concentrate on those areas of DNA that do not undergo recombination. Two particular regions of DNA are particularly suitable, firstly mitochondrial DNA and secondly the nonrecombining region of the Y chromosome.

Mitochondrial DNA (mtDNA) is found in the mitochondria, which are small organelles located in the cytoplasm of cells. Each cell may have thousands of mitochondria. These are thought to have originated as independent organisms that entered into a symbiotic relationship with more complex cells 1.5 billion years ago. They have lost most of their genes to the nuclear DNA, but the 37 genes left are involved in the production of energy. MtDNA is inherited maternally - it is not transmitted by males to the next generation (although there have been some controversial papers published about the possible paternal transmission of mtDNA - if it happens, it must be an extremely rare occurrence and has little or no impact on population studies). MtDNA does not undergo recombination, so any mutations acquired in the past in its DNA sequence are maintained. Two noncoding (i. e., they do not contain genes) regions of mtDNA are studied which seem to accumulate single base mutations at a high rate - hypervariable regions I and II (HVR I and HVR II). These mutations are inherited together and form a set of DNA markers that have been classified into haplotypes by comparison to a reference mtDNA sequence (the Cambridge Reference Sequence). A number of similar haplotypes forms a haplogroup. By assuming that mutations are acquired at a regular rate, the concept of a ‘molecular clock’ can be applied and the date of the appearance of new mtDNA hap-logroups can be estimated (also known as divergence or coalescence times) albeit with wide confidence limits.

MtDNA from human, animal, and plant populations around the globe has been classified in this way. The relationships between the different haplogroups have been studied by means of phylogenetic analysis, most notably by network analysis. MtDNA has been used to study the evolution of modern humans in Africa, and the movements of these people into the Old World (Out of Africa). mtDNA has also been used to re-examine the Wave of Advance hypothesis developed to explain the spread of agriculture from its origins in the Near East into Europe. In both research questions there were opposing hypotheses that predicted differing genetic outcomes for human populations. In both research areas, there was controversy between the accepted archaeological interpretation and the genetically based interpretation. In this article, the nature of the controversies will be explored and the importance of the genetic contribution to the debate will be stressed. In both cases, the contribution of genetics has led to a better understanding of the complex issues involved in these two most important events of human prehistory. Our knowledge of these events would be the poorer without mtDNA analysis (see DNA: Ancient).

The nonrecombining region of the Y chromosome is also making its contribution to our understanding of human population history. Only mammalian males possess the Y chromosome (at least, the vast majority do - there are always rare exceptions to every rule in biology) and it is inherited paternally. The nonrecombining region of the Y chromosome contains the SRY gene which determines maleness, but it also contains a number of DNA markers which can be inherited as a block, that is, a haplotype. Analysis and classification of Y chromosome haplogroups started somewhat later than the mtDNA work. The nature of the Y DNA markers is more complex than the single base mutations found in mtDNA, so the phylogenetic analysis is also more complicated and the molecular clock concept more difficult to apply. However, the male side of human population history tells a broadly similar story for Out of Africa, although the story is not so clear-cut for the Mesolithic/Neolithic transition in Europe; hence, the details of this research will not be dealt with in this article.